------------------------------------------------------------------------ CAT12.8.1 r2040: 1/1: ./sub-0025472/ses-1/sub-0025472_ses-1_run-1_T1w.n ------------------------------------------------------------------------ SANLM denoising (medium): 25s APP: Rough bias correction: Initialize 5s Estimate background 4s Initial correction 4s Refine background 2s Final correction 4s Final scaling 4s 28s Correct center-of-mass 2s Affine registration 8s SPM preprocessing 1 (estimate 1 - TPM registration): 26s Use previous fine affine registration. 51s SPM preprocessing 1 (estimate 2): 65s SPM preprocessing 2 (write): Write Segmentation 15s Update Segmentation 18s Update Skull-Stripping 36s Update probability maps 8s 77s Global intensity correction: 13s SANLM denoising after intensity normalization (medium): 20s Fast Optimized Shooting registration 26s Local adaptive segmentation (LASstr=0.50): Prepare maps 3s Prepare partitions 2s Prepare segments (LASmod = 1.00) 11s Estimate local tissue thresholds (WM) 15s Estimate local tissue thresholds (GM) 21s Intensity transformation 0s SANLM denoising after LAS (medium) 35s 90s ROI segmentation (partitioning): Atlas -> subject space 6s Major structures 3s Ventricle detection 10s Blood vessel detection 7s WMH detection (WMHCstr=0.50 > WMHCstr'=0.04) 19s Manual stroke lesion detection 0s Closing of deep structures 1s Side alignment 3s Final corrections 4s 52s Blood vessel correction (BVCstr=0.50): 2s Amap using initial SPM12 segmentations (MRF filter strength 0.06): 27s AMAP peaks: [CSF,GM,WM] = [0.360.06,0.680.07,0.980.05] Final cleanup (gcutstr=0.25): Level 1 cleanup (ROI estimation) 3s Level 1 cleanup (brain masking) 2s Level 2 cleanup (CSF correction) 1s Level 3 cleanup (CSF/WM PVE) 2s 9s Optimized Shooting registration with 2.50:-0.25:1.50 mm (regstr=0.50): Template: "/code/SPM/MCR_Linux/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NLin2009cAsym/Template_0_GS.nii" 1 | 2.50 | 0.0854 0.0000 0.0854 | 32.0000 2 | 2.50 | 0.0826 0.0012 0.0838 | 29.4886 3 | 2.50 | 0.0817 0.0019 0.0836 | 26.9772 4 | 2.50 | 0.0813 0.0021 0.0834 | 24.6107 5 | 2.50 | 0.0809 0.0023 0.0832 | 22.6548 6 | 2.50 | 0.0807 0.0024 0.0830 | 20.6989 7 | 2.50 | 0.0804 0.0025 0.0828 | 18.9688 8 | 2.50 | 0.0800 0.0026 0.0826 | 17.4455 9 | 2.50 | 0.0797 0.0027 0.0824 | 15.9223 10 | 2.50 | 0.0794 0.0028 0.0822 | 14.6627 11 | 2.50 | 0.0791 0.0029 0.0819 | 13.4764 12 | 2.50 | 0.0787 0.0029 0.0816 | 12.3015 13 | 2.50 | 0.0784 0.0030 0.0814 | 11.3776 14 | 2.50 | 0.0780 0.0031 0.0811 | 10.4537 15 | 2.25 | 0.0781 0.0032 0.0813 | 9.5920 16 | 2.25 | 0.0752 0.0046 0.0799 | 8.8725 17 | 2.25 | 0.0740 0.0052 0.0792 | 8.1530 29 | 2.00 | 0.0758 0.0024 0.0782 | 3.3283 30 | 2.00 | 0.0700 0.0048 0.0748 | 3.1221 31 | 2.00 | 0.0680 0.0058 0.0737 | 2.9160 43 | 1.75 | 0.0670 0.0033 0.0703 | 1.5785 44 | 1.75 | 0.0625 0.0056 0.0682 | 1.5194 45 | 1.75 | 0.0610 0.0065 0.0675 | 1.4626 57 | 1.50 | 0.0598 0.0047 0.0645 | 1.0900 58 | 1.50 | 0.0566 0.0068 0.0634 | 1.0730 59 | 1.50 | 0.0555 0.0076 0.0630 | 1.0579 Shooting registration with 2.50:-0.25:1.50 mm takes: 137s Prepare output 8s 146s Jacobian determinant (RMS): 0.011 0.042 0.063 0.086 0.109 | 0.116953 Template Matching: 0.085 0.222 0.204 0.183 0.166 | 0.166452 Write result maps: 31s Surface and thickness estimation: lh: Thickness estimation (0.50 mm): WM distance: 34s CSF distance: 11s PBT2x thickness: 34s 84s Create initial surface 65s Topology correction: 79s Surface refinement: 83s Reduction of surface collisions with optimization: 60s Spherical mapping with areal smoothing 68s Spherical registration 200s rh: Thickness estimation (0.50 mm): WM distance: 30s CSF distance: 12s PBT2x thickness: 34s 81s Create initial surface 67s Topology correction: 79s Surface refinement: 75s Reduction of surface collisions with optimization: 55s Spherical mapping with areal smoothing 74s Spherical registration 237s Final surface processing results: Average thickness (FS): 2.3520  0.6623 mm Surface intensity / position RMSE: 0.0725 / 0.0759 Euler number / defect number / defect size: 36.0 / 24.0 / 1.15% Display thickness: /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/surf/lh.thickness.sub-0025472_ses-1_run-1_T1w Display thickness: /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/surf/rh.thickness.sub-0025472_ses-1_run-1_T1w Show surfaces in orthview: /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/sub-0025472_ses-1_run-1_T1w.nii Surface ROI estimation: 9s Surface and thickness estimation takes: 1391s ROI estimation in native space: ROI estimation of 'cobra' atlas 21s ROI estimation of 'neuromorphometrics' atlas 86s ROI estimation of 'lpba40' atlas 26s ROI estimation of 'hammers' atlas 60s ROI estimation of 'thalamus' atlas 5s ROI estimation of 'ibsr' atlas 23s ROI estimation of 'aal3' atlas 38s ROI estimation of 'mori' atlas 52s ROI estimation of 'anatomy3' atlas 70s ROI estimation of 'julichbrain' atlas 90s ROI estimation of 'Schaefer2018_100Parcels_17Networks_order' atlas 36s ROI estimation of 'Schaefer2018_200Parcels_17Networks_order' atlas 61s ROI estimation of 'Schaefer2018_400Parcels_17Networks_order' atlas 116s ROI estimation of 'Schaefer2018_600Parcels_17Networks_order' atlas 133s ROI estimation of 'Tian_Subcortex_S2_7T' atlas 11s Write results 12s 830s Quality check: 10s Print 'Graphics' figure to: /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/report/catreport_sub-0025472_ses-1_run-1_T1w.pdf ------------------------------------------------------------------------ CAT preprocessing takes 50 minute(s) and 43 second(s). Image Quality Rating (IQR): 77.84% (C+) GM volume (GMV): 44.71% (721.03 / 1612.62 ml) GM thickness (GMT): 2.35  0.66 mm Segmentations are saved in /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/mri Reports are saved in /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/report Labels are saved in /var/lib/condor/execute/dir_578211/ds/IACAS/sub-0025472/ses-1/label ------------------------------------------------------------------------